Introduction
Origin: Something to work on before I had full access to lab (aka covid project).
Goals:
- Phylogenomic analysis of Phaeocystis
- Does a phylogenomic approach recapitulate taxonomies derived from the 18S gene?
- Genomic biogeography of Phaeocystis
- Do metagenomic data reveal finer-scale biogeographic patterns in Phaeocystis global distribution?
- Is there geographic differentiation at the strain, sub-strain, or snp level?
- Functional biogeography of Phaeocystis
- Do metatranscriptomic data show biogeographic patterns in Phaeocystis gene expression?
- Is expression of certain genes linked to locations or environmental conditions?
Background:
Phaeocystis is a globally occurring haptophyte phytoplanktom genus that causes algal blooms in many locations. Blooms are often considered nuisance blooms or harmful blooms due to large amounts of sulfur-based molecules produced, as well as seafoam.
In addition to being a fascinating and ecologically important phytoplankton genus, Phaeocystis is a good test case for probing the limits of tara data since we have a priori knowledge about where species should be found.
18S v4-based distribution pattern of Phaeocystis species.
The data
- 2 jgi geneomes
- 4 MMETSP transcriptomes
- 3 transcriptomes sequences as part of my thesis research
BUSCO

Orthogroups


Tree
Fasttree based on 61 single-copy core genes:

this phylogeny perfectly matches the 18S-gene-based phylogeny.
Tara Read Mapping
Against all genes:
a.k.a. the stumbling block

Inconcistent patterns between data-types:
- P. antarctica is more dominent in metaG data (jgi genome and caron isolate MMETSP)
- P. antarctica genes that recruit in the N. atlantic and are annotated are also annotated in the other species data
- P. globosa ccmp1528 overwhelmingly recruits the majority of the metaT reads
Against single-copy core genes (SCGs):

- P. jahnii really pops out in this analysis
- the situation is improved in the metaT 0.8-5 µm size fraction … but not the others
Intercomparison between data types
SMALL size fraction

Micromonas
Another globally distributed phytoplankton genus. Sanity check!
Data
- 2 jgi genomes
- 4 MMETSP transcriptomes
tree
## busco
Tara Read Mapping
- Inconsistency again - MMETSP1327 pops out in metaT, but not the G v T pattern as much as in the Phaeocystis results
Intercomparison between data types

Outlook
Pre-Antarctica:
- finish vitamin trial (thanks for all the help so far!!!)
- P. pouchetii reference transcriptome sequencing
In Antarctica
- wirte P. globosa microbiome paper
- collect samples fpr metaT to complement Van Mooy lipidomic samples, collect surface water flowthrough transects for metaT/metaP, collect P. antarctica colonies for microbiome analysis and new cultures, trace metal (iron and B12) bottle enrichment experiment
Post Antarctica:
- RNA and protein extractions from cruise and year one of CCB time series
- start P. pouchetii and P. antarctica microbiome experiments